All the SA user config files (like .user_prefs) are created by ispconfig as owner "root".
As spamd/spamc changes the running user to the mailbox owner it is not able to write those config files or tmp/lock files into the .spamassassin directory.
I don't know what further effects this could have (aside from writing lots of permission denied entries to the mail log).

@falko/till: would it be possible to make ispconfig2 change the ownership of those files and the directory to the mailbox owner?
This should not be a problem even if you don't use spamd/spamc.